Merge pull request #28 from mcara/fix-new-table

Fix for removed 'new_table'
spacetelescope · Jan 19, 2017 · a7e1a95 · a7e1a95
2 parents 4f56c9c + dcd20b7
commit a7e1a95
Show file tree

Hide file tree

Showing 3 changed files with 30 additions and 30 deletions.
diff --git a/commissioning/basecase.py b/commissioning/basecase.py
@@ -24,7 +24,7 @@ def hasSkyLines(self):
             return True
         else:
             return False
-        
+
     def setglobal(self,fname=None):
         if fname is None:
             fname=__file__
@@ -37,7 +37,7 @@ def setglobal(self,fname=None):
         dirname=os.path.dirname(self.name)
         if not os.path.isdir(dirname):
             os.makedirs(dirname)
-            
+
         self.file=self.name
         self.thresh=0.01
         self.superthresh=0.20
@@ -64,7 +64,7 @@ def setglobal(self,fname=None):
             self.tda['form']=self.form
         except AttributeError:
             pass
-        
+
         self.tra={}
 
     def run_crbox(self,spstring,form,output="",wavecat="INDEF",
@@ -79,7 +79,7 @@ def run_crbox(self,spstring,form,output="",wavecat="INDEF",
                        form=form,
                        wavecat=wavecat,
                        output=output)
-        
+
 
     def run_countrate(self,form,output=None):
         if output is None:
@@ -97,7 +97,7 @@ def run_countrate(self,form,output=None):
 
         if count == 10:
             raise(e)
-        
+
     def runpy(self):
         self.sptest=etc.parse_spec(self.spectrum)
         self.csname=self.name+'.fits'
@@ -138,7 +138,7 @@ def count_outliers(self,Nsigma=3):
         std=self.adiscrep.std()
         outliers=N.where(abs(self.adiscrep) > mean + Nsigma*std)
         return len(outliers[0])
-    
+
     def arraytest(self,test,ref):
         #Exclude the endpoints where the gradient is very steep
         self.adiscrep=self.arraydiff(test,ref)#[2:-2]
@@ -171,7 +171,7 @@ def savepysyn(self,wave,flux,fname,units=None):
             ytype='flux'
         col1=pyfits.Column(name='wavelength',format='D',array=wave)
         col2=pyfits.Column(name=ytype,format='D',array=flux)
-        tbhdu=pyfits.new_table(pyfits.ColDefs([col1,col2]))
+        tbhdu=pyfits.BinTableHDU.from_columns(pyfits.ColDefs([col1,col2]))
         tbhdu.header.update('tunit1','angstrom')
         tbhdu.header.update('tunit2',units)
         tbhdu.writeto(fname.replace('.fits','_pysyn.fits'))
@@ -203,7 +203,7 @@ def testcrspec(self):
 
         if count == 10:
             raise e
-        
+
         os.unlink(wname)
 
         #Now do the comparison
@@ -212,7 +212,7 @@ def testcrspec(self):
         rflux=spref.flux[ridx]
         tflux=self.sptest(spref.wave[ridx])
         self.arraysigtest(tflux,rflux)
-        
+
 class calcphotCase(calcspecCase):
     Extrap=None
     def runpy(self):
@@ -228,10 +228,10 @@ def runpy(self):
             except OSError:
                 pass
         self.discrep=-99
-
 
-
-
+
+
+
     def testthru(self):
         iraf.calcband(obsmode=self.obsmode,output=self.cbname)
         ref=S.FileBandpass(self.cbname)
@@ -241,7 +241,7 @@ def testthru(self):
         self.savepysyn(rwave,tthru,self.cbname)
         self.arraysigtest(tthru,rthru)
 
-        
+
     def testefflam(self):
         iraf.calcphot(obsmode=self.obsmode,spectrum=self.spectrum,
                       form='photlam', func='efflerg')
@@ -286,10 +286,10 @@ def testthru(self):
         __test__ = False
     def testefflam(self):
         __test__ = False
-        
+
 
 class thermbackCase(calcspecCase):
-        
+
     def runpy(self):
 
         #self.sptest=etc.parse_spec(self.spectrum)
@@ -334,7 +334,7 @@ def testcrspec(self):
 ##         if N.any(self.sp.wave != ref.wave):
 ##             raise ValueError('wave arrays not equal')
 ##         self.arraysigtest(self.sp.flux,ref.flux)
-        
+
     def testthermback(self):
         iraf.thermback(obsmode=self.obsmode,form='counts')
         rtherm=iraf.thermback.getParam('thermback.thermflux',native=1)
@@ -378,7 +378,7 @@ def testcrphotlam(self):
         tflux=obs.binflux[tidx]
         self.savepysyn(obs.binwave,obs.binflux,
                        self.crname,units='photlam')
-        
+
         self.arraysigtest(tflux,rflux)
 
     def testcrcounts(self):
@@ -395,7 +395,7 @@ def testcrcounts(self):
                        units='counts')
         if N.any(obs.binwave != spref.wave):
             raise ValueError('wave arrays not equal')
-        
+
         self.arraysigtest(tflux,rflux)
 
     def testcountrate(self):

diff --git a/commissioning/doscalars.py b/commissioning/doscalars.py
@@ -13,7 +13,7 @@ def getdata(dirpath,fieldname,instr,save=True):
     nfiles=len(flist)
     if nfiles == 0:
         raise ValueError('No files found')
-    
+
     val=N.zeros((nfiles,),dtype=N.float64)
     obsmode=N.zeros((nfiles,),dtype=N.float64)
     spectrum=N.zeros((nfiles,),dtype=N.float64)
@@ -26,7 +26,7 @@ def getdata(dirpath,fieldname,instr,save=True):
     scount=0
     namedict={}
     i=0
-    
+
     #
     # Start processing
     for fname in flist:
@@ -45,7 +45,7 @@ def getdata(dirpath,fieldname,instr,save=True):
             sdict[sp]=scount
             scount+=1
         spectrum[i]=sdict[sp]
-        
+
         try:
             val[i]=float(d['tra_discrep'])
         except KeyError:
@@ -68,7 +68,7 @@ def getdata(dirpath,fieldname,instr,save=True):
         c5=pyfits.Column(name='discrep',format='D',
                          array=val)
 
-        tbhdu=pyfits.new_table(pyfits.ColDefs([c1,c2,c3,c4,c5]))
+        tbhdu=pyfits.BinTableHDU.from_columns(pyfits.ColDefs([c1,c2,c3,c4,c5]))
         outname=os.path.join(os.path.abspath(os.path.dirname(dirpath)),
                              "%s_%s_table.fits"%(instr,fieldname))
         tbhdu.writeto(outname,clobber=True)
@@ -87,7 +87,7 @@ def plotdata(obsmode,spectrum,val,odict,sdict,
              instr,fieldname,outdir,outname):
     isetting=P.isinteractive()
     P.ioff()
-    
+
     P.clf()
     P.plot(obsmode,val,'.')
     P.ylabel('(pysyn-syn)/syn')
@@ -105,7 +105,7 @@ def plotdata(obsmode,spectrum,val,odict,sdict,
     matplotlib.interactive(isetting)
 
 def run(dirpath, fieldname, instr):
-    
+
     namedict,odict,sdict,obsmode,spectrum,val = getdata(dirpath,
                                                         fieldname,
                                                         instr)

diff --git a/commissioning/extrap/extrap.py b/commissioning/extrap/extrap.py
@@ -40,7 +40,7 @@ def run(fname,outdir=None):
 
     if outdir is not None and not os.path.isdir(outdir):
         os.mkdir(outdir)
-        
+
     dwave=0.001
     f=pyfits.open(fname)
     nonparam,error=classify_file(f)
@@ -59,7 +59,7 @@ def run(fname,outdir=None):
     if ok:
         f.close()
         return "%s: no change necessary"%fname
-    
+
 
     #If not ok, we fall through to here.
     #We're going to have to make a new hdu
@@ -93,7 +93,7 @@ def run(fname,outdir=None):
         clist.append(tc)
 
     #Now we have all the columns; put them in an HDU
-    tbhdu=pyfits.new_table(clist)
+    tbhdu=pyfits.BinTableHDU.from_columns(clist)
     #and copy in the header information we need
     h=f[1].header.copy()
     h.update('NAXIS1',tbhdu.header['NAXIS1'])
@@ -125,7 +125,7 @@ def blue(fname,outdir=None):
     """Cut&pasted from run, but to operate only on blue end."""
     if outdir is not None and not os.path.isdir(outdir):
         os.mkdir(outdir)
-        
+
     dwave=0.001
     f=pyfits.open(fname)
     nonparam,error=classify_file(f)
@@ -144,7 +144,7 @@ def blue(fname,outdir=None):
     if ok:
         f.close()
         return "%s: no change necessary"%fname
-    
+
 
     #If not ok, we fall through to here.
     #We're going to have to make a new hdu
@@ -178,7 +178,7 @@ def blue(fname,outdir=None):
         clist.append(tc)
 
     #Now we have all the columns; put them in an HDU
-    tbhdu=pyfits.new_table(clist)
+    tbhdu=pyfits.BinTableHDU.from_columns(clist)
     #and copy in the header information we need
     h=f[1].header.copy()
     h.update('NAXIS1',tbhdu.header['NAXIS1'])